Re: Constant z axis

From: Chris Harrison (charris5_at_gmail.com)
Date: Sat Oct 11 2008 - 22:59:31 CDT

Navdeep,

This isn't presently possible in NAMD. You can set x and y to a constant
area and allow fluctuations in z, but the inverse isn't possible in the
current code. Can you explain why you would want to do this? What type of
simulation would benefit from an ability to freeze cell fluctuations in z
but not those of x & y?

Chris

On Sat, Oct 11, 2008 at 10:25 PM, Navdeep <navdeep79_at_gmail.com> wrote:

> Hi Chris
>
>
>
> Actually my question was: I want to keep the z-axis of the Unit Cell
> constant and let only xand y axis to vary while running a NPT simulation.
> How can I do that.
>
>
>
> Thanks a lot,
>
> Navdeep
>
>
>
> *From:* Chris Harrison [mailto:charris5_at_gmail.com]
> *Sent:* Saturday, October 11, 2008 5:14 PM
> *To:* Nd S
> *Cc:* NAMD list
> *Subject:* Re: namd-l: Constant z axis
>
>
>
> Navdeep,
>
> To keep z-axis coords of atoms fixed:
> Option 1: Look at section 6.1.1 of the manual. Specifically,
> "selectConstrZ".
>
> Option 2: Look at Tclforces in the manual (and then the online tutorial at
> http://www.ks.uiuc.edu). You can create a restraint (with large force
> constant) to hold atoms frozen (effectively).
>
> Chris
>
>
> On Wed, Oct 8, 2008 at 7:59 PM, Nd S <navdeep79_at_gmail.com> wrote:
>
> Hi all
>
> I am doing NPT simulation.
>
> My questions are:
> 1. I want to keep the z-axis constant, how I can do that.
> 2. Do I have to use "useGroupPressure" if some atoms in the box are fixed,
> or I can use the default settings.
>
> Thanks a lot,
> Navdeep
>
>
>
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> char_at_ks.uiuc.edu Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
> Fax: 217-244-6078
>

-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078

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